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by claude@2026-07, 2026-07-03
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The paper uses comparative genomics across three annual–perennial pairs of Oryza species to investigate the evolutionary basis of the perennial-to-annual transition. It identifies 91 gene families that are present in all perennial species but missing in at least one annual counterpart, and links their predicted functions to physiological aspects of perenniality including phenology, energy allocation, and source–sink dynamics. A comparative co-expression analysis suggests these gene families may also regulate processes that differ between perennial and annual Oryza, such as reproduction, root development, and environmental responses. The main limitation stated in the paper is that functional roles are inferred from annotation and functional prediction rather than direct experimental validation. The paper does not explicitly discuss endometriosis or adenomyosis; it was included in the corpus via a keyword match in the upstream search index.
Abstract
Perennial rice has shown great potential for alleviating multidimensional sustainability issues that are prevalent in current rice agriculture, prompting widespread interest in its breeding. Currently, one major hurdle for these breeding efforts is our scarce knowledge about the evolutionary mechanisms of the perennial-to-annual transition in Oryza . Here, by performing comparative genomics of three annual-perennial pairs of Oryza species ( Oryza rufipogon / O. nivara , O. glumaepatula / O. glaberrima , and O. meyeriana / O. brachyantha ), we identified 91 gene families that are present in all the perennial species but are missing in any of the annual species. Annotations and functional prediction of these gene families demonstrated that they may be associated with a battery of physiological components of perenniality, such as phenology, energy allocation, and source–sink dynamics. Furthermore, comparative co-expression analysis revealed that many of these families may also play important regulatory roles for orchestrating diverse processes that differ between perennial and annual Oryza species, including reproduction, root development, and response to environmental stimuli. These results highlight the potential complexity of the emergence of annuality in the Oryza genus and offer promising candidates for future functional studies.
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Abstract
Perennial rice has shown great potential for alleviating multidimensional sustainability issues that are prevalent in current rice agriculture, prompting widespread interest in its breeding. Currently, one major hurdle for these breeding efforts is our scarce knowledge about the evolutionary mechanisms of the perennial-to-annual transition in Oryza. Here, by performing comparative genomics of three annual-perennial pairs of Oryza species (Oryza rufipogon/O. nivara, O. glumaepatula/O. glaberrima, and O. meyeriana/O. brachyantha), we identified 91 gene families that are present in all the perennial species but are missing in any of the annual species. Annotations and functional prediction of these gene families demonstrated that they may be associated with a battery of physiological components of perenniality, such as phenology, energy allocation, and source–sink dynamics. Furthermore, comparative co-expression analysis revealed that many of these families may also play important regulatory roles for orchestrating diverse processes that differ between perennial and annual Oryza species, including reproduction, root development, and response to environmental stimuli. These results highlight the potential complexity of the emergence of annuality in the Oryza genus and offer promising candidates for future functional studies.
Competing Interest Statement
The authors have declared no competing interest.
Data Availability
All data supporting the conclusions of this article are provided within the article or in the supplementary material.
List of abbreviations
- CPM
- Counts per million
- GO
- Gene ontology
- IPPT
- Isopentenyl pyrophosphate transferase
- KEGG
- Kyoto Encyclopedia of Genes and Genomes
- NCBI
- National centre for biotechnology information
- SRA
- Sequence read archive
- STAG
- Species tree from all genes
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